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Semantic physical science

Edited by:
Dr Peter Murray-Rust, Henry Rzepa

In January 2012 we held an invited workshop (hackathon) and symposium to investigate and formalise the use of semantics in physical sciences (“Semantic Physical Science” or “SPS”). Although the primary concentration is on physical, instrumental and computational chemistry, many of the principles and tools relate to other sciences rich in numeric data. The primary technologies are based on chemical markup language (CML) and, very recently, MathML, and we show that it is possible to create fully semantic declarative scientific objects. The papers in this series represent the outputs of a number of leading groups e.g. CSIRO, PNNL, STFC, Kitware, IUCr, the Blue Obelisk and the Unilever Centre for Molecular Science Informatics (who hosted the meeting.) The papers will be published by the journal asynchronously involving the normal process of peer-review.

The papers in this series represent the outputs of a number of leading groups e.g. CSIRO, PNNL, STFC, Kitware, IUCr, the Blue Obelisk and the Unilever Centre for Molecular Science Informatics (who hosted the meeting.) The papers will be published by the journal asynchronously involving the normal process of peer-review.

We thank the EPSRC for a "Pathways to Impact" award which funded the workshop and also the Cambridge-related article processing charges.

Readers should also consult our earlier thematic series, "Visions of a Semantic Molecular Future", which laid the groundwork last year for much of the basis of the workshop.

An attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal is presented, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5.

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.